Bugfix/official naming

Created by: magaliruffier

Requirements

• Filling out the template is required. Any pull request that does not include enough information to be reviewed in a timely manner may be closed at the maintainers' discretion;
• Review the contributing guidelines for this repository; remember in particular:
  • do not modify code without testing for regression
  • provide simple unit tests to test the changes
  • if you change the schema you must patch the test databases as well, see Updating the schema
  • the PR must not fail unit testing

Description

Using one or more sentences, describe in detail the proposed changes. The transcript name extension is overwritten every time a new loop is started. This results in all transcripts having -201 as an extension, rather than -201, -202 within the same gene. This bugfix re-establishes the former behaviour.

Use case

Describe the problem. Please provide an example representing the motivation behind the need for having these changes in place. All transcripts within the same gene have the same name. This means it is harder to distinguish between transcripts without using the stable ID.

Benefits

If applicable, describe the advantages the changes will have. Transcripts within the same gene have the same name.

Possible Drawbacks

If applicable, describe any possible undesirable consequence of the changes. Users rely on the transcript name and expect it to be stable, which it is fundamentally not.

Testing

Have you added/modified unit tests to test the changes? The whole pipeline was run and results compared with previous run.

If so, do the tests pass/fail? Results are comparable.

Have you run the entire test suite and no regression was detected?